Related papers: Polyply: a python suite for facilitating simulatio…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Thermodynamic models are often vital when characterising complex systems, particularly natural gas, electrolyte, polymer, pharmaceutical and biological systems. However, their implementations have historically been abstruse and cumbersome,…
Polymers-macromolecular systems composed of repeating chemical units-constitute the molecular foundation of living organisms, while their synthetic counterparts drive transformative advances across medicine, consumer products, and energy…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…
Navigating rigid body objects through crowded environments can be challenging, especially when narrow passages are presented. Existing sampling-based planners and optimization-based methods like mixed integer linear programming (MILP)…
Material node graphs are programs that generate the 2D channels of procedural materials, including geometry such as roughness and displacement maps, and reflectance such as albedo and conductivity maps. They are essential in computer…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…
Space-filling experimental design techniques are commonly used in many computer modeling and simulation studies to explore the effects of inputs on outputs. This research presents raxpy, a Python package that leverages expressive annotation…
Effective hydrodynamic modeling is crucial for accurately predicting fluid-particle interactions in diverse fields such as biophysics and materials science. Developing and implementing hydrodynamic algorithms is challenging due to the…
Distributed, large-scale quantum computing will need architectures that combine matter-based qubits with photonic links, but today's software stacks target either gate-based chips or linear-optical devices in isolation. We introduce Optyx,…
Granular materials are of critical interest to many robotic tasks in planetary science, construction, and manufacturing. However, the dynamics of granular materials are complex and often computationally very expensive to simulate. We…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
QAssemble is a pure-Python package for the quantum many-body problem. It implements various functional approaches, such as tight-binding, Hartree-Fock, and GW approximations within a unified object-oriented architecture. Each physical…
We present a novel, generally applicable Monte Carlo algorithm for the simulation of fluid systems. Geometric transformations are used to identify clusters of particles in such a manner that every cluster move is accepted, irrespective of…
Polymer materials have the characteristic feature that they are multiscale systems by definition. Already the description of a single molecules involves a multitude of different scales, and cooperative processes in polymer assemblies are…
We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived…
DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large…
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…